Regulation of restriction endonuclease activity with antibiotics

'Star' activity and complete loss of specificity of CeqI endonuclease

Restriction endonuclease CeqI, an isoschizomer of EcoRV, exhibits 'star' activity, a relaxation of specificity in the presence of Mn2+, dimethyl sulphoxide or glycerol. The enzyme cleaves a set of sequences that differ from the canonical GATATC by only one nucleotide in positions 2, 3, 4 or 5. Two of these sequences are not cleaved if modified by dam methylase. A further loss of specificity can be observed in circumstances less favourable for the enzyme, namely low-ionic-strength buffers of pH values below 6.0 or above 9.4. This activity seems to cleave DNA at any sequence, producing a smear instead of well-defined bands. Partial renaturation of the denatured enzyme gives rise to a similar non-specific nuclease activity.

Structural and sequence-dependent aspects of drug intercalation into nucleic acids

Information gained from X-ray crystallographic studies on drug-nucleic acid complexes is described, with emphasis on the intercalation process. Relevant data from NMR experiments are examined in order to highlight similarities and differences between solution and solid-state structures. Theoretical analyses of intercalation complexes are also discussed and evaluated, with respect to the structural methods, with special reference being made to nucleic acid conformation and positions of drug molecules in the binding sites.

Protection of (dA.dT) cluster regions in the DNAase I cleavage of DNA by specific interaction with netropsin

The specific DNA binding ligand netropsin selectively blocks dA-dT base pairs in clusters containing two or more consecutive thymine residues at the dNAase I cleavage sites of DNA. Using CD and UV absorption measurements it is shown, that at various ratios of netropsin to nucleotide concentrations and even at satuation of ligand interaction the enzyme cuts along regions containing dG-dC pairs sandwiched between dA-dT pairs. This follows a slow kinetics and is associated with a release of netropsin from those segments. These facts suggests the usefulness of the partial protection of certain DNA sequences in DNAase I cleavage sites in producing DNA fragments in structural studies of the genome. A possible interpretation of the effect of netropsin binding on the enzymatic hydrolysis of phosphodiester bonds of the helix is discussed.